Metagenomic surveillance uncovers diverse and novel viral taxa in febrile patients from Nigeria
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Published:2023-08-04
Issue:1
Volume:14
Page:
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ISSN:2041-1723
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Container-title:Nature Communications
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language:en
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Short-container-title:Nat Commun
Author:
Oguzie Judith U.ORCID, Petros Brittany A.ORCID, Oluniyi Paul E.ORCID, Mehta Samar B., Eromon Philomena E., Nair Parvathy, Adewale-Fasoro Opeoluwa, Ifoga Peace Damilola, Odia Ikponmwosa, Pastusiak Andrzej, Gbemisola Otitoola Shobi, Aiyepada John Oke, Uyigue Eghosasere Anthonia, Edamhande Akhilomen Patience, Blessing Osiemi, Airende Michael, Tomkins-Tinch ChristopherORCID, Qu James, Stenson Liam, Schaffner Stephen F.ORCID, Oyejide Nicholas, Ajayi Nnenna A.ORCID, Ojide Kingsley, Ogah Onwe, Abejegah Chukwuyem, Adedosu Nelson, Ayodeji Oluwafemi, Liasu Ahmed A., Okogbenin Sylvanus, Okokhere Peter O., Park Daniel J.ORCID, Folarin Onikepe A.ORCID, Komolafe Isaac, Ihekweazu Chikwe, Frost Simon D. W., Jackson Ethan K., Siddle Katherine J.ORCID, Sabeti Pardis C.ORCID, Happi Christian T.ORCID
Abstract
AbstractEffective infectious disease surveillance in high-risk regions is critical for clinical care and pandemic preemption; however, few clinical diagnostics are available for the wide range of potential human pathogens. Here, we conduct unbiased metagenomic sequencing of 593 samples from febrile Nigerian patients collected in three settings: i) population-level surveillance of individuals presenting with symptoms consistent with Lassa Fever (LF); ii) real-time investigations of outbreaks with suspected infectious etiologies; and iii) undiagnosed clinically challenging cases. We identify 13 distinct viruses, including the second and third documented cases of human blood-associated dicistrovirus, and a highly divergent, unclassified dicistrovirus that we name human blood-associated dicistrovirus 2. We show that pegivirus C is a common co-infection in individuals with LF and is associated with lower Lassa viral loads and favorable outcomes. We help uncover the causes of three outbreaks as yellow fever virus, monkeypox virus, and a noninfectious cause, the latter ultimately determined to be pesticide poisoning. We demonstrate that a local, Nigerian-driven metagenomics response to complex public health scenarios generates accurate, real-time differential diagnoses, yielding insights that inform policy.
Funder
U.S. Department of Health & Human Services | NIH | National Institute of Allergy and Infectious Diseases TED’s Audacious Project, including the ELMA Foundation, MacKenzie Scott, the Skoll Foundation, and Open Philanthropy The World Bank ACE019 and ACE-IMPACT U.S. Department of Health & Human Services | NIH | National Institute of General Medical Sciences Howard Hughes Medical Institute (HHMI) TED’s Audacious Project, including the ELMA Foundation, MacKenzie Scott, the Skoll Foundation, and Open Philanthropy
Publisher
Springer Science and Business Media LLC
Subject
General Physics and Astronomy,General Biochemistry, Genetics and Molecular Biology,General Chemistry,Multidisciplinary
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